So I'm looking at your process to kinda get how it works, it's not one I've really done, so I was assuming that you started with grayscale and then added color to it, but it sounds like instead you are starting with color and then using a luminosity filter to turn the second layer white? I've never used this technique before, so forgive me, I thought you were using a different technique. Disregard what I said, because if you put a layer set to color on top of another color that isn't gray (since your color layer is on the bottom) it will just mess up your colors.
So, what I would do is instead of duplicating the color layer, to just use a clipping layer. That way you don't need to worry about luminosity at all. You can do a gray scale in this layer, but in a way where black is black and white is transparent. That way you can use "lock transparent pixels" to turn whatever gray in the layer into a warmer burgandy that won't alter your color layer or turn it gray.
The gray layer that I've seen people use is to map out where the ambient occlusion is. (in fact the artist, Nicholas Kole, does this a lot, so you should check out his twitter to see how he does it because he makes videos on his process.) "ambient occlusion." is wherever you have a place light cannot reach, that will be a shadow that is black and not the tint of a color.
It's not the same as a hard shadow cast from a light source, which will generally take on the tint of the sky or the warmth of skin (skin is quite warm!) because of reflected light.